Contacts of the helix formed by residues 682 - 718 (chain D) in PDB entry 5EOA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 682 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 3.8 24.9 - - + +
41A LEU* 4.3 8.2 - - - +
678C PRO* 5.4 5.7 - - + +
679D SER* 3.1 34.8 - - - +
680D SER 2.8 15.2 + - - +
681D ASN* 1.3 74.6 - - - +
683D LEU* 1.3 54.9 + - - +
684D VAL 3.3 0.4 - - - -
685D GLU* 3.1 3.0 + - - +
686D MET* 2.7 47.2 + - - +
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Residues in contact with LEU 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 3.8 13.9 - - + -
35B PHE 3.7 21.5 - - - +
36B THR* 4.8 2.7 - - - -
37B PRO* 4.4 22.7 - - + -
40B LEU* 4.0 33.4 - - + -
678C PRO* 5.6 5.6 - - + -
679D SER* 2.6 44.7 + - - +
682D THR* 1.3 71.4 + - - +
684D VAL* 1.3 57.2 + - - +
686D MET* 3.1 6.1 + - - +
687D THR* 2.6 38.6 + - - -
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Residues in contact with VAL 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ASN* 6.2 0.2 - - - +
34B THR* 3.6 28.2 - - + +
680D SER* 3.6 18.8 - - - +
681D ASN* 3.5 25.6 - - - +
683D LEU* 1.3 75.6 - - - +
685D GLU* 1.3 65.6 + - - +
687D THR* 3.6 3.4 + - - +
688D LEU* 3.0 28.6 + - + +
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Residues in contact with GLU 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.7 26.4 - - + +
681D ASN* 3.0 41.1 + - - +
682D THR 3.1 5.2 + - - +
683D LEU 3.1 0.8 - - - -
684D VAL* 1.3 82.8 - - - +
686D MET* 1.3 61.9 + - - +
688D LEU* 3.2 24.0 + - - +
689D GLY* 2.9 25.8 + - - -
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Residues in contact with MET 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PRO* 3.5 33.2 - - + +
40A LEU* 3.5 38.8 - - + -
41A LEU* 3.9 10.5 - - + -
44A MET* 3.6 24.8 - - + +
40B LEU* 3.7 33.0 - - + -
678C PRO* 6.4 0.2 - - + -
683C LEU* 5.2 2.7 - - + -
682D THR* 2.7 27.6 + - - +
683D LEU* 3.7 10.3 - - - +
685D GLU* 1.3 72.3 - - - +
687D THR* 1.3 53.6 + - - +
689D GLY* 3.1 1.7 + - - -
690D MET* 2.7 40.7 + - - +
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Residues in contact with THR 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP 3.9 21.8 - - - +
34B THR* 3.9 1.1 - - - +
35B PHE* 2.9 57.8 + - + +
40B LEU* 4.4 1.3 - - - +
683D LEU* 2.6 23.2 + - - -
684D VAL* 3.6 6.7 - - - +
686D MET* 1.3 72.9 - - - +
688D LEU* 1.3 62.9 + - - +
690D MET* 3.3 2.0 + - - +
691D LYS* 3.0 38.8 + - + +
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Residues in contact with LEU 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D VAL* 3.0 16.9 + - + +
685D GLU* 3.5 25.4 - - - +
687D THR* 1.3 76.4 - - - +
689D GLY* 1.3 57.4 + - - +
691D LYS* 3.2 11.7 + - + +
692D LYS* 3.0 65.5 + - + +
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Residues in contact with GLY 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 5.9 0.7 - - - -
44A MET* 4.6 21.2 - - - +
45A LYS* 5.9 5.8 - - - -
48A LEU* 5.4 3.2 - - - +
685D GLU 2.9 14.5 + - - -
686D MET 3.5 2.9 - - - -
688D LEU* 1.3 76.1 - - - +
690D MET* 1.3 58.1 + - - +
692D LYS* 3.5 9.8 + - - +
693D LEU* 3.1 31.0 + - - +
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Residues in contact with MET 690 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.8 30.7 - - + +
35B PHE* 4.5 12.8 - - + -
40B LEU* 4.1 11.4 - - + +
43B GLN* 3.8 13.3 - - + +
44B MET* 3.4 50.7 - - + +
47B LEU* 3.8 23.3 - - + +
686C MET* 4.0 10.1 - - + -
690C MET* 5.5 0.2 - - - +
686D MET 2.7 25.7 + - - +
687D THR 3.8 3.8 - - - +
689D GLY* 1.3 72.5 - - - +
691D LYS* 1.3 62.6 + - - +
693D LEU* 3.7 8.6 + - - +
694D LYS* 3.2 22.7 + - - +
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Residues in contact with LYS 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP* 4.3 31.1 + - - +
35B PHE* 3.8 30.5 - - + -
43B GLN* 5.5 1.8 - - - +
687D THR* 3.0 27.9 + - + +
688D LEU* 3.6 11.2 - - + +
690D MET* 1.3 77.2 - - - +
692D LYS* 1.3 64.7 + - - +
694D LYS* 3.4 8.9 + - + +
695D GLU* 3.1 24.6 + - - +
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Residues in contact with LYS 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 4.7 10.7 - - - +
48A LEU* 3.8 31.7 - - + +
688D LEU* 3.0 58.3 + - + +
689D GLY* 3.9 5.8 - - - +
691D LYS* 1.3 74.5 - - + +
693D LEU* 1.3 59.5 + - - +
695D GLU* 3.3 7.3 + - - +
696D GLU* 2.9 32.7 + - - +
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Residues in contact with LEU 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 4.5 13.7 - - + +
47A LEU* 3.9 41.1 - - + +
48A LEU* 3.9 16.7 - - + +
51A ASN* 3.6 28.9 - - + +
47B LEU* 4.0 22.2 - - + -
690C MET* 4.8 0.9 - - + -
693C LEU* 5.0 3.4 - - + -
689D GLY 3.1 18.8 + - - +
690D MET* 3.8 14.8 - - - +
691D LYS 3.4 0.2 - - - -
692D LYS* 1.3 75.3 - - - +
694D LYS* 1.3 62.6 + - - +
696D GLU* 3.3 1.6 + - - +
697D MET* 2.9 37.2 + - - +
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Residues in contact with LYS 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLN* 3.9 20.8 + - - +
46B GLU* 3.3 33.3 + - - -
47B LEU* 3.8 20.6 - - + +
50B LYS* 4.2 12.6 + - + +
690D MET 3.2 16.2 + - - +
691D LYS* 3.6 9.2 - - + +
692D LYS 3.3 0.2 - - - -
693D LEU* 1.3 79.4 - - - +
695D GLU* 1.3 64.2 + - - +
697D MET* 3.4 3.0 + - - +
698D GLU* 3.0 44.5 + - - +
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Residues in contact with GLU 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 5.7 0.2 - - - -
691D LYS 3.1 14.8 + - - +
692D LYS* 3.6 7.1 - - - +
694D LYS* 1.3 79.1 - - - +
696D GLU* 1.3 65.6 + - - +
698D GLU* 3.0 29.8 + - - +
699D GLY* 3.1 9.4 + - - -
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Residues in contact with GLU 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.9 18.5 - - + +
51A ASN* 3.8 12.6 - - + +
52A HIS* 3.0 55.9 + - - +
55A LYS* 3.1 27.8 + - - +
692D LYS 2.9 17.5 + - - +
693D LEU 3.6 4.9 - - - +
695D GLU* 1.3 78.3 - - - +
697D MET* 1.3 56.8 + - - +
699D GLY* 3.0 16.8 + - - -
700D VAL* 3.2 13.7 + - - +
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Residues in contact with MET 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 3.4 24.5 - - - +
47B LEU* 3.6 30.1 - - + +
50B LYS* 4.1 13.9 - - + -
51B ASN* 3.1 51.6 - - + +
54B LEU* 5.6 6.9 - - + +
693C LEU* 5.6 3.1 - - + -
693D LEU* 2.9 33.4 + - - +
694D LYS* 3.8 4.3 - - - +
696D GLU* 1.3 72.7 - - - +
698D GLU* 1.3 65.1 + - - +
699D GLY 3.1 0.2 - - - -
700D VAL* 3.3 10.3 + - + +
701D VAL* 3.1 29.1 + - + +
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Residues in contact with GLU 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 3.8 24.5 + - + +
694D LYS* 3.0 31.7 + - - +
695D GLU* 3.0 26.9 + - - +
697D MET* 1.3 79.0 - - - +
699D GLY* 1.3 55.8 + - - +
701D VAL* 3.7 7.6 + - - +
702D LYS* 3.2 36.6 + - + +
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Residues in contact with GLY 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 3.5 20.7 - - - +
695D GLU 3.1 7.1 + - - -
696D GLU 3.0 9.5 + - - -
698D GLU* 1.3 77.0 - - - +
700D VAL* 1.3 62.0 + - - +
702D LYS* 3.2 22.6 - - - +
703D GLU* 3.2 16.8 + - - +
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Residues in contact with VAL 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 3.9 12.1 - - - +
54A LEU* 3.8 12.6 - - + -
55A LYS* 3.6 36.6 - - + +
58A MET* 3.8 24.4 - - + +
54B LEU* 3.5 34.1 - - + -
696D GLU 3.2 9.9 + - - +
697D MET* 3.6 9.2 - - - +
699D GLY* 1.3 74.2 - - - +
701D VAL* 1.3 67.4 + - - +
702D LYS 3.1 1.1 - - - -
703D GLU* 3.0 5.1 + - - +
704D LEU* 2.9 21.5 + - - +
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Residues in contact with VAL 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LYS* 5.9 3.8 - - + +
54B LEU* 4.4 21.1 - - + -
697D MET* 3.1 18.3 + - + +
698D GLU* 3.8 8.5 - - - +
700D VAL* 1.3 76.6 - - - +
702D LYS* 1.3 64.8 + - + +
704D LEU* 3.4 9.4 + - + +
705D ALA* 3.0 25.0 + - + +
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Residues in contact with LYS 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698D GLU* 3.2 24.7 + - + +
699D GLY* 3.2 15.3 - - - +
700D VAL 3.1 0.2 - - - -
701D VAL* 1.3 81.0 - - + +
703D GLU* 1.3 67.5 + - + +
705D ALA* 3.3 8.3 + - - +
706D GLU* 3.2 20.8 + - - +
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Residues in contact with GLU 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 4.0 14.5 - - + +
58A MET* 3.6 23.3 - - + -
59A LYS* 3.2 46.5 - - + +
62A ASN* 2.9 32.4 + - - +
699D GLY 3.2 14.8 + - - +
700D VAL 3.0 6.3 + - - +
702D LYS* 1.3 77.0 - - - +
704D LEU* 1.3 60.2 + - - +
706D GLU* 3.4 3.1 + - - +
707D ASN* 2.9 26.2 + - - +
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Residues in contact with LEU 704 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 4.4 8.8 - - + -
54B LEU* 3.8 21.1 - - + -
57B ALA* 3.6 31.4 - - + +
58B MET* 4.0 18.2 - - + -
61B ASN* 3.6 38.1 - - + +
700D VAL 2.9 10.9 + - - +
701D VAL* 3.6 11.7 - - + +
703D GLU* 1.3 73.3 - - - +
705D ALA* 1.3 55.5 - - - +
707D ASN* 3.0 6.6 + - + +
708D ASN* 2.8 45.0 + - - +
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Residues in contact with ALA 705 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701D VAL* 3.0 16.2 + - + +
702D LYS* 3.4 12.3 - - - +
704D LEU* 1.3 76.1 - - - +
706D GLU* 1.3 62.3 + - - +
708D ASN* 3.2 10.6 + - - +
709D HIS* 3.0 21.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 706 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 3.4 28.7 - - + +
66A LYS* 3.1 33.1 + - - -
702D LYS 3.2 9.1 + - - +
703D GLU* 3.5 4.5 - - - +
705D ALA* 1.3 77.6 - - - +
707D ASN* 1.3 62.9 + - - +
709D HIS* 3.1 16.5 + - - +
710D ILE* 3.0 30.2 + - + +
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Residues in contact with ASN 707 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A MET* 6.5 0.9 - - + -
61A ASN* 4.7 4.6 - - - +
62A ASN* 2.7 28.4 + - - +
65A MET* 4.2 24.3 - - - +
61B ASN* 2.8 30.8 + - - +
65B MET* 4.9 0.9 - - - +
707C ASN* 4.3 14.3 + - - -
703D GLU 2.9 12.1 + - - +
704D LEU* 3.0 13.2 + - + +
706D GLU* 1.3 77.0 - - - +
708D ASN* 1.3 57.3 + - - +
710D ILE* 3.3 6.2 + - - +
711D LEU* 3.0 35.6 + - - +
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Residues in contact with ASN 708 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 5.2 4.2 + - - +
60B LEU* 6.3 0.2 - - - +
61B ASN* 2.9 32.5 + - - +
64B ALA* 5.1 2.4 - - - +
704D LEU* 2.8 30.4 + - - +
705D ALA* 3.5 10.3 - - - +
707D ASN* 1.3 75.1 - - - +
709D HIS* 1.3 60.2 + - - +
711D LEU* 3.4 10.4 + - - +
712D GLU* 3.0 28.9 + - - +
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Residues in contact with HIS 709 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705D ALA 3.0 12.3 + - - +
706D GLU* 3.1 21.9 + - - +
708D ASN* 1.3 77.0 - - - +
710D ILE* 1.3 69.9 + - + +
712D GLU* 3.0 24.4 + - + +
713D ARG* 3.2 52.8 + - + +
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Residues in contact with ILE 710 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASN* 3.8 19.5 - - - +
65A MET* 4.0 20.0 - - + +
66A LYS* 3.7 39.5 - - + +
69A PHE* 5.1 7.9 - - + -
706D GLU* 3.0 29.5 + - + +
707D ASN* 3.8 6.5 - - - +
708D ASN 3.3 0.2 - - - -
709D HIS* 1.3 83.5 - - + +
711D LEU* 1.3 64.0 + - - +
713D ARG* 3.1 11.4 + - + +
714D PHE* 3.0 41.9 + - + -
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Residues in contact with LEU 711 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 3.5 24.5 - - + -
61B ASN* 3.3 44.0 - - - +
64B ALA* 3.9 15.0 - - + -
65B MET* 3.7 20.9 - - + -
68B ARG* 2.8 51.4 + - + +
714C PHE* 4.9 1.3 - - + -
707D ASN* 3.0 17.0 + - - +
708D ASN* 3.5 12.6 - - - +
710D ILE* 1.3 77.1 - - - +
712D GLU* 1.3 60.9 + - - +
714D PHE* 3.4 12.7 + - + +
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Residues in contact with GLU 712 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 3.9 18.4 + - - +
708D ASN 3.0 14.3 + - - +
709D HIS* 3.0 17.6 + - + +
711D LEU* 1.3 75.5 - - - +
713D ARG* 1.3 65.5 + - + +
715D GLY* 3.0 13.9 + - - -
716D SER* 3.3 12.5 + - - +
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Residues in contact with ARG 713 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.8 30.7 - - + -
709D HIS* 3.4 47.2 + - + +
710D ILE* 3.1 11.1 + - - +
712D GLU* 1.3 75.5 - - - +
714D PHE* 1.3 66.7 + - - +
716D SER* 2.9 24.0 + - - -
717D LEU* 2.9 9.9 + - - -
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Residues in contact with PHE 714 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 3.7 45.1 - - + -
68A ARG* 4.3 1.6 - - + -
69A PHE* 3.9 25.8 - + + -
72A LEU* 3.7 16.2 - - + -
68B ARG* 4.1 14.8 - - + -
72B LEU* 3.5 39.1 - - + +
714C PHE* 3.6 18.4 - + - -
710D ILE* 3.0 35.6 + - + -
711D LEU* 3.4 13.0 - - + +
713D ARG* 1.3 77.5 - - - +
715D GLY* 1.3 58.4 + - - +
717D LEU* 2.9 29.4 + - + +
718D THR* 3.5 10.4 + - - +
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Residues in contact with GLY 715 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG* 3.4 37.9 - - - +
71B GLU* 4.0 4.9 - - - -
712D GLU 3.0 7.6 + - - -
714D PHE* 1.3 78.6 - - - +
716D SER* 1.3 60.5 + - - +
718D THR* 3.3 10.2 + - - -
719D MET* 3.1 27.5 - - - +
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Residues in contact with SER 716 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712D GLU* 3.3 10.3 + - - +
713D ARG* 2.9 22.9 + - - -
715D GLY* 1.3 74.9 - - - +
717D LEU* 1.3 64.8 + - - +
718D THR 3.3 0.2 - - - -
719D MET* 3.5 23.7 + - - +
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Residues in contact with LEU 717 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 4.0 28.5 - - + +
72A LEU* 3.9 28.9 - - + -
73A SER* 4.0 25.4 - - - +
76A THR* 4.7 3.6 - - + -
72B LEU* 4.5 9.4 - - + -
75B TRP* 3.7 30.5 + - + -
713D ARG 2.9 7.3 + - - +
714D PHE* 2.9 16.5 + - + +
716D SER* 1.3 79.4 - - - +
718D THR* 1.3 60.4 + - + +
719D MET 3.1 9.8 + - - +
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Residues in contact with THR 718 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B GLU* 4.1 27.1 + - + +
72B LEU* 3.7 29.8 - - + -
75B TRP* 3.8 41.6 - - + +
714D PHE 4.0 5.2 - - - +
715D GLY 3.3 13.2 + - - -
716D SER 3.3 0.6 - - - -
717D LEU* 1.3 74.8 - - - +
719D MET* 1.3 69.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il